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protocols::qsar::scoring_grid::HbaGrid Class Reference

#include <HbaGrid.hh>

Inheritance diagram for protocols::qsar::scoring_grid::HbaGrid:
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Collaboration diagram for protocols::qsar::scoring_grid::HbaGrid:
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Public Member Functions

 HbaGrid ()
 
virtual ~HbaGrid ()
 
virtual void refresh (core::pose::Pose const &pose, core::Vector const &center, core::Size const &ligand_chain_id_to_exclude)
 populate the grid with values based on a passed pose More...
 
virtual void refresh (core::pose::Pose const &pose, core::Vector const &center)
 populate the grid with values based on a passed pose More...
 
virtual void refresh (core::pose::Pose const &pose, core::Vector const &center, utility::vector1< core::Size > ligand_chain_ids_to_exclude)
 populate the grid with values based on a passed pose More...
 
virtual core::Real score (core::conformation::Residue const &residue, core::Real const max_score, qsarMapOP qsar_map)
 return the current score of a residue using the current grid More...
 
virtual core::Real atom_score (core::conformation::Residue const &residue, core::Size atomno, qsarMapOP qsar_map)
 return the current score of an atom using the current grid More...
 
virtual utility::json_spirit::Value serialize ()
 serialize the SingleGrid to a json_spirit object More...
 
virtual void deserialize (utility::json_spirit::mObject data)
 deserialize a json_spirit object to a SingleGrid More...
 
void parse_my_tag (utility::tag::TagPtr const tag)
 setup a grid based on RosettaScripts input More...
 
- Public Member Functions inherited from protocols::qsar::scoring_grid::SingleGrid
 SingleGrid (std::string type)
 
virtual ~SingleGrid ()
 
virtual void initialize (core::Vector const &center, core::Real width, core::Real resolution)
 initialize a grid of zeros with a given centerpoint, width and resolution (in angstroms). More...
 
virtual void set_chain (char chain)
 set the chain around which to calculate the grid More...
 
char get_chain ()
 get the chain around which the grid is calculated More...
 
core::grid::CartGrid
< core::Real > const & 
get_grid ()
 return a constant reference to the grid More...
 
void set_type (std::string type)
 set the grid type More...
 
virtual std::string get_type ()
 return the grids type More...
 
void set_center (core::Vector center)
 set the center of the grid More...
 
core::Vector get_center ()
 get the center of the grid More...
 
core::Real get_min_value () const
 get the max score value in the grid More...
 
core::Real get_max_value () const
 get the minimum score value in the grid More...
 
core::Real get_point (core::Real x, core::Real y, core::Real z)
 get the value of a single point in the grid based on pdb coordinates More...
 
core::Real get_point (core::Vector coords)
 get the value of a single point in the grid based on pdb coordinates More...
 
numeric::xyzVector< core::Sizeget_dimensions ()
 get dimensions of the grid More...
 
core::Vector get_pdb_coords (int x, int y, int z)
 get the pdb coordinates based on grid point coordinates More...
 
core::Vector get_pdb_coords (core::grid::CartGrid< core::Real >::GridPt gridpt)
 get the pdb coordinates based on grid point coordinates More...
 
void grid_to_kin (utility::io::ozstream &out, core::Real min_val, core::Real max_val, core::Size stride)
 
virtual bool is_in_grid (core::conformation::Residue const &residue)
 check to see if residue is in grid More...
 
std::list< std::pair
< core::Vector, core::Real > > 
get_point_value_list_within_range (core::Real lower_bound, core::Real upper_bound, core::Size stride)
 
virtual void dump_BRIX (std::string const &prefix)
 output a BRIX formatted grid. This really does not work well but is being left for legacy purposes More...
 
void set_sphere (core::Vector const &coords, core::Real radius, core::Real value)
 
void set_ring (core::Vector const &coords, core::Real inner_radius, core::Real outer_radius, core::Real value)
 
void diffuse_ring (core::Vector const &coords, core::Real radius, core::Real width, core::Real magnitude)
 
void set_distance_sphere (core::Vector const &coords, core::Real cutoff)
 
void set_point (core::Vector const &coords, core::Real value)
 
void set_distance_sphere_for_atom (core::Real const &atom_shell, core::Vector const &coords, core::Real cutoff)
 
void set_score_sphere_for_atom (numeric::interpolation::spline::InterpolatorOP lj_spline, core::Vector const &coords, core::Real cutoff)
 
void fill_with_value (core::Real)
 the entire grid with some value More...
 
- Public Member Functions inherited from protocols::qsar::scoring_grid::GridBase
 GridBase ()
 
virtual ~GridBase ()
 

Private Attributes

numeric::interpolation::spline::InterpolatorOP lj_spline_
 

Constructor & Destructor Documentation

protocols::qsar::scoring_grid::HbaGrid::HbaGrid ( )

References lj_spline_.

protocols::qsar::scoring_grid::HbaGrid::~HbaGrid ( )
virtual

Member Function Documentation

core::Real protocols::qsar::scoring_grid::HbaGrid::atom_score ( core::conformation::Residue const &  residue,
core::Size  atomno,
qsarMapOP  qsar_map 
)
virtual
void protocols::qsar::scoring_grid::HbaGrid::deserialize ( utility::json_spirit::mObject  data)
virtual

deserialize a json_spirit object to a SingleGrid

Reimplemented from protocols::qsar::scoring_grid::SingleGrid.

References protocols::qsar::scoring_grid::SingleGrid::deserialize(), and lj_spline_.

void protocols::qsar::scoring_grid::HbaGrid::parse_my_tag ( utility::tag::TagPtr const  tag)
virtual

setup a grid based on RosettaScripts input

Implements protocols::qsar::scoring_grid::SingleGrid.

void protocols::qsar::scoring_grid::HbaGrid::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center,
core::Size const &  ligand_chain_id_to_exclude 
)
virtual

populate the grid with values based on a passed pose

Implements protocols::qsar::scoring_grid::SingleGrid.

Referenced by refresh().

void protocols::qsar::scoring_grid::HbaGrid::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center 
)
virtual
void protocols::qsar::scoring_grid::HbaGrid::refresh ( core::pose::Pose const &  pose,
core::Vector const &  center,
utility::vector1< core::Size ligand_chain_ids_to_exclude 
)
virtual

populate the grid with values based on a passed pose

Implements protocols::qsar::scoring_grid::SingleGrid.

References refresh().

core::Real protocols::qsar::scoring_grid::HbaGrid::score ( core::conformation::Residue const &  residue,
core::Real const  max_score,
qsarMapOP  qsar_map 
)
virtual
utility::json_spirit::Value protocols::qsar::scoring_grid::HbaGrid::serialize ( )
virtual

serialize the SingleGrid to a json_spirit object

Reimplemented from protocols::qsar::scoring_grid::SingleGrid.

References lj_spline_, and protocols::qsar::scoring_grid::SingleGrid::serialize().

Member Data Documentation

numeric::interpolation::spline::InterpolatorOP protocols::qsar::scoring_grid::HbaGrid::lj_spline_
private

The documentation for this class was generated from the following files: